tbuckley/cabot-search huggingface dataset:
BIOM-31. TEMPOROSPATIAL PROTEIN PROFILING OF HUMAN GLIOBLASTOMAS REVEALS MOLECULAR MECHANISMS AND BIOMARKERS UNDERLYING RESPONSES TO IMMUNE CHECKPOINT INHIBITION
Authors: Jacob S Young, Calixto-Hope Lucas, Kyounghee Seo, Minh Nguyen, William Chen, David A Solomon, Mitchel S Berger, Joanna J Phillips, Manish Aghi, David Raleigh
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanisms underlying ICI responses are incompletely understood. Thus, serial glioblastoma samples are valuable resources for identifying biomarkers or therapeutic targets to increase the efficacy of ICI in patients with glioblastoma. We obtained paired glioblastoma samples from 7 patients who underwent sequential surgery, ICI, and eventual salvage surgery for recurrence. Patients were distinguished as ICI responders (n=3) or non-responders (n=4) based on (1) MRI evidence of tumor stability/reduction over 6+ months after ICI, or (2) pathologic evidence of predominant treatment effect at the time of salvage surgery after ICI. FFPE sections from each tumor (n=14) were stained using H&amp;E or IHC/IF for macrophages/microglia (CD68) or T cells (CD3) and analyzed using light or fluorescence microscopy. Six regions-of-interest (ROIs) comprising viable tumor were selected neuropathologist from each sample (n=84 ROIs). ROIs were analyzed using quantitative spatial profiling of 72 proteins on the Nanostring Digital Profiler platform. Glioblastomas responding to ICI were enriched in T-cell proteins (CD3, CD4, CD8) and T-cell activation markers (CD25) at the time of salvage compared to initial surgery. Markers of MAPK signaling were suppressed in pre-ICI samples compared to post-ICI samples in responders. p-ERK was suppressed in post-ICI samples compared to pre-ICI samples in non-responders. Myeloid proteins (CD68, CD163, CD11c) were enriched in post-ICI samples compared to pre-ICI samples in non-responders. Principle components analysis revealed p-ERK and immune proteins (CD3, CD4, CD8, CD20, CD11c, CTLA4, CD68, CD45, CD56, and CD127) accounted for 62% of the variance among pre-ICI and post-ICI samples in responders. In conclusion, temporospatial protein profiling of human glioblastomas reveals molecular mechanisms and biomarkers underlying responses to immune checkpoint inhibition. These data establish a foundation for functional studies to reprogram the immunosuppressive glioblastoma microenvironment and sensitize tumors to immune checkpoint inhibition.
DISP-04. PATIENTS WITH PROGRESSION OF SPINE METASTASES WHO PRESENT TO CLINIC HAVE BETTER OUTCOMES COMPARED TO THOSE WHO PRESENT TO THE EMERGENCY DEPARTMENT
Authors: Michael Strong, Varun Kathawate, Peyton Goethe, Lila Tudrick, Joseph Linzey, Ayobami Ward, Mark Zaki, Rushikesh Joshi, William Jackson, Nicholas Szerlip
Journal: Neuro-Oncology (2022)

Abstract As cancer therapies have improved, survival has increased. Spine metastases are becoming more common in the course of oncologic disease. Complications arising from these metastases have a significant impact on patient quality of life and the optimal method to follow these patients and avoid deficits has not yet been adequately studied. The purpose of this study was to identify characteristics of a subgroup of oncologic patients with metastatic spinal disease. Retrospective analysis of oncological patients ( &amp;gt; 18 years) who underwent stereotactic body radiation therapy (SBRT) to the spine at the University of Michigan, from 2010 to 2020 was performed. A total of 395 radiographic isocenters in 298 patients were identified. Of these, 112 isocenters in 83 patients and 283 isocenters in 215 patients were treated after presenting to the ED or clinic, respectively. As expected, patients presenting to the ED had more deficits compared to the clinic (severe pain (30% vs 6%); difficulty ambulating (48% vs 8%); weakness (25% vs 6%); or myelopathy (11% vs 1%). Social economic factors including marital status, insurance type, and having a primary care physician were similar between groups. Of the 112 ED isocenters, 58 required surgery plus SBRT (52%); while 54 required SBRT only (48%). Additionally, of the 283 clinic isocenters, 53 required surgery plus SBRT (19%); while 230 only required SBRT (81%). The overall survival was higher for clinic compared to ED (12.6mos vs 8.5mos), respectively. Interestingly, even when surgical intervention was taken into consideration, those presenting to the ED still had poorer outcomes compared to clinic (6.7mos vs 13.3mos), respectively. Metastatic spinal disease patients who present to the ED have poorer survival than those who present to the clinic. A better understanding of the factors that drive this phenomenon is warranted in order to improve the management and outcomes of this population.
DDDR-40. OVERCOMING DRUG RESISTANCE BY TARGETING AUTOPHAGY REGULATED BY A LONG INTERGENIC NONCODING RNA
Authors: Alexander Zhang, Zhi Sheng, Kevin Pridham
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Autophagy is a self-eating process that supports cancer cell survival. Autophagy activation during drug treatment often prolongs cancerous cell survival, causing drug resistance, as seen in glioblastoma multiforme (GBM) to temozolomide (TMZ). Thus, blocking autophagy is an appealing approach to overcoming cancer drug resistance. Long noncoding RNAs (LincRNAs) have emerged as potential targets. LincRNA LINC00467 (renamed ARLINC) was recently identified as a potential autophagy inhibitor in cancer cells. However, ARLINC’s mechanism of inhibition and whether its modulation can suppress autophagy in cancer remains unknown. OBJECTIVE Research Question: Can blocking autophagy restore the sensitivity of cancer cells to chemotherapy? Hypotheses: 1) ARLINC regulates chemotherapy drug sensitivity by inducing autophagy. 2) Overexpression of ARLINC can increase chemotherapy drug sensitivity, as measured by cell viability and autophagy assays METHODS Aim 1) Endogenous ARLINC levels in GBM cell lines will be measured using qRT-PCR. Aim 2) Cell viability of GBM upregulated with pBabe-ARLINC (experiment) and pBabe (control) then exposed to increasing concentrations of TMZ will be analyzed using MTS assay. Student’s T-test will be used to determine significance. Aim 3) Autophagy flux will be measured in GBM lines that are transiently transfected with ARLINC compared to the empty vector via Cyto-ID assay. RESULTS Aim 1: Compared to Normal Human Astrocytes (NHA), U87MG had higher levels, LN18 and SF295 and lower, and LN229 had around the same levels of ARLINC. Aim 2: MTS cell viability assays in SF295 upregulated with ARLINC showed no significant decrease in TMZ sensitivity. Aim 3: Cyto-ID in U87MG and LN229 upregulated with ARLINC showed no significant decrease in autophagy flux. CONCLUSIONS/FUTURE WORK Results show no effect of ARLINC upregulation on cell viability and autophagy flux. Future work involves knockdown experiments to decrease intracellular levels of ARLINC and determine the effects of upregulation of autophagy on sensitization.
EPCO-15. LINKING HISTOLOGICAL GLIOBLASTOMA PHENOTYPES TO TRANSCRIPTIONAL SUBTYPES AND PROGNOSIS USING DEEP LEARNING
Authors: Thomas Roetzer-Pejrimovsky, Barbara Kiesel, Karl-Heinz Nenning, Johanna Klughammer, Martin Rajchl, Christoph Bock, Johannes Hainfellner, Bernhard Baumann, Georg Langs, Adelheid Woehrer
Journal: Neuro-Oncology (2022)

Abstract Deep learning is increasingly utilized in medical image analysis and shows promise to substantially inform treatment decisions in clinical practice. While it finds broad applications in radiology or genomics, there are still relatively few applications of deep learning to the analysis of histological images. A disease in which a better understanding of underlying phenotype-genotype correlations seems crucial is glioblastoma, the most common malignant brain tumor in adults that features a dismal prognosis and limited therapeutic options. Using a large cohort of 276 glioblastoma patients with available histological, immunohistochemical, clinical and molecular data, we trained an Xception convolutional neural network to predict patient survival and transcriptional subtypes on histological images alone. We used 5-fold cross validation to evaluate the performance of the trained network. We achieve a high accuracy for predicting overall survival on univariable (p &amp;lt; 0.001) and multivariable (p = 0.01) analysis. Moreover, we observe a high accuracy for predicting the predominant transcriptional subtype with an AUC of 0.84, 0.81, and 0.71 for classical, mesenchymal and proneural subtypes, respectively (all p &amp;lt; 0.001). Finally, we plot heatmaps of the predicted transcriptional subtype and risk scores to directly link them to the histological phenotypes and the tumor microenvironment. Reassuringly, we find an association of the mesenchymal subtype with the perinecrotic niche and of the proneural subtype with the infiltrating edge. In conclusion, we introduce an easily adaptable convolutional neural network model for working with histological data, which can accurately predict outcomes and transcriptional subtypes in glioblastoma.
EPID-04. IMPACT OF SEX DIFFERENCES IN IRON SUPPLEMENTATION AND OUTCOMES IN ANEMIC GLIOBLASTOMA PATIENTS
Authors: Ganesh Shenoy, Chachrit Khunsriraksakul, Kondaiah Palsa, Vladimir Khristov, Justin Lathia, Jill Barnholtz-Sloan, James Connor
Journal: Neuro-Oncology (2022)

Abstract We performed a retrospective sex-stratified analysis on 1750 histologically confirmed surgical glioblastoma patients (737 female, 1013 male) diagnosed between January 1, 2000 – January 1, 2020 in the TriNetX Research Network. Among 737 female glioblastoma patients, 140 (18.99%) were classified as anemic (defined as having mean 5-year-post-diagnosis hemoglobin levels &amp;lt; 12 g/dL). Among 1013 male patients, 177 (17.4%) were classified as anemic (mean 5-year-post-diagnosis hemoglobin levels &amp;lt; 13 g/dL). Of the 140 anemic female patients, 30 (21.4%) received iron supplementation whereas 28 (15.8%) of 177 anemic male patients received iron supplementation. Anemic female patients receiving iron supplementation were on average younger than anemic female patients who did not receive supplementation (mean age at diagnosis (SD): 59.08 vs. 64.87, p = 0.037), however no statistically significant differences in presence of chemotherapy administration, radiation administration, or Charlson comorbidity index (CCI) were detected. Anemic male patients receiving iron supplementation had no significant difference in mean age at diagnosis, chemotherapy administration, radiation administration, or CCI compared to anemic male patients not receiving iron supplementation. Kaplan-Meier analysis revealed that iron supplementation in anemic female patients was associated with prolonged overall median survival (536 vs. 361 days, p = 0.03) whereas iron supplementation in anemic male patients was not associated with any significant increase in overall survival (392 vs. 361 days, p = 0.89). Multivariate analysis using a Cox proportional hazards model adjusted for mean 5-year-post-diagnosis hemoglobin levels, age at diagnosis, chemotherapy administration, radiation administration, and CCI revealed that iron supplementation was associated with improved survival in anemic female patients (HR: 0.53, 95% CI: 0.30 – 0.96) but not in anemic male patients (HR: 0.87, 95% CI: 0.54 – 1.43). These results highlight the importance of iron biology in glioblastoma and provide evidence for further investigation into iron supplementation of anemic glioblastoma patients.
IMMU-29. PERIPHERAL VACCINATION WITH GIFT-7 SECRETING TUMOR CELLS AUGMENTS AGE RELATED THYMIC DECLINE AND IMPROVES SURVIVAL ACROSS MULTIPLE GLIOBLASTOMA MOUSE MODELS
Authors: Jack Shireman, Lei Zhao, Xiaohu Wang, Jacques Galipeau, Mahua Dey
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM), the most common primary brain tumor in adults, has a dismal prognosis and nearly 100% recurrence rate. With a median age of diagnosis of 64, age associated immune dysfunction needs to be accounted for during treatment. Cannonically, immunotherapies target checkpoint signaling pathways in order to create T-cell populations that are resistant to exhaustion. Our lab has demonstrated that exhaustion is not the only factor at play regarding T-cell dysfunction, as patients with GBM have a robust CD8+CD28- effector population present both in the blood and tumor, possibly indicating T-cell senescence. Here we present research utilizing GIFT-7, a fusiokine combining GMCSF and IL-7, which has been demonstrated to combat age related thymic decline. To accurately understand this phenomenon in the context of aging all experiments were done in mice aged 52 weeks before intial tumor injection. We transfected the mouse glioma line GL261 cells to stably express and secrete GIFT-7 and injected 500k cells (GIFT7/VC) subcutaneously in the flank of B6 mice. This flank tumor allowed both for continued systemic administration of GIFT7, as well as immune exposure to the tumor similar to a vaccine model. After 4 weeks an intracranial challenge of normal GL261 cells was conducted and survival was monitored. Mice with GIFT-7 flanks had a larger population of CD3 and CD4 T-cells in their systemic circulation (p &amp;lt; .001 and p &amp;lt; .05 respectively). We also observed that the GIFT-7 flank mice demonstrated an increased tendency to have T-cells of all populations (CD3, CD4+, and CD8+) present within the brain. Finally, GIFT-7 flank mice survival was vastly improved with 60% of mice showing long term survival ( &amp;gt; 120 days) compared to 0 VC mice.
DDDR-25. CO-INHIBITION OF KINASE SIGNALING PATHWAYS AND EPIGENETIC REGULATORS OVERCOMES COMPENSATORY EFFECTS IN PEDIATRIC HIGH-GRADE GLIOMAS
Authors: Jack Adams, Lea Stitzlein, Melissa Singh, Xiaoping Su, Yue Lu, Cavan Bailey, Michelle Monje, Christopher Whitehead, Judith Sebolt-Leopold, Joya Chandra
Journal: Neuro-Oncology (2022)

Abstract Pediatric high-grade gliomas (pHGG) confer poor survival outcomes with minimal treatment options due to a high rate of therapeutic resistance and few surgical options. One subgroup of pHGG is diffuse intrinsic pontine glioma (DIPG). Patient-derived cell lines, such as SU-DIPG-XIII, SU-DIPG-VI, and SU-DIPG-IV, recapitulate epigenetic mutations seen in patients. In these lines, lysine-specific demethylase 1 (LSD1) is overexpressed and knockdown/inhibition slows growth, therefore, optimizing LSD1 inhibitor treatment regimens is promising. In other models, MEK kinase activation acts as a mechanism of resistance to LSD1 inhibitors. This is relevant to DIPG due to the frequency of dysregulated and mutated upstream kinase pathways. Thus, we sought to identify the connection between LSD1 and kinase signaling as a therapeutic co-inhibition strategy in DIPG. Pharmacologically relevant catalytic LSD1 inhibitors were assessed using the alamarBlue viability assay and demonstrated wide ranges of IC₅₀ values with ORY-1001(19 μM to &amp;gt; 150 μM), ORY-2001( &amp;gt; 50 μM), GSK-LSD1(134 μM to &amp;gt; 500 μM), and IMG-7289(1.6 μM-179 μM) in the SU-DIPG lines. Resistance mechanisms from kinase modulation were investigated via Western Blot to determine if kinase inhibition could sensitize these cells to LSD1 inhibition. We discovered that LSD1 inhibition caused an unexpected increase in pAKT and pERK, suggesting enhanced activity of protumorigenic kinases. To overcome kinase activation from LSD1 inhibition, MEK or PI3K inhibitors, including selumetinib, trametinib, and BKM120, were tested. A novel dual kinase inhibitor directed against EGFR and PI3K, MTX-241F, was also assessed. Several combinations caused a significant increase in efficacy measured by cell viability. We further observed that the addition of kinase inhibitors with LSD1 inhibition decreased phosphorylated kinases. Overall, the combination enhanced in vitro efficacy in contrast to single-agent inhibition supporting an interplay between LSD1 and kinase signaling in pHGG. Future studies will assess this combination utilizing orthotopic xenograft models of DIPG
DISP-06. POPULATION-LEVEL DETERMINANTS OF SOCIO-DEMOGRAPHIC, TUMOR, AND TREATMENT FACTORS IN GLIOBLASTOMA USING SEER DATABASE (1997-2016)
Authors: Wonsuk Yoo, Michael Garcia, William Kennedy, Nader Sanai
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Although socio-demographic and treatment factors have been separately linked to impact on prognosis in several GBM studies, no studies to date have collectively evaluated many potential individual patient and treatment-related factors and their impact on survival in GBM in a comprehensive, multi-institutional, population-based manner. The purpose of this study is to identify sociodemographic, tumor, treatment, and clinical characteristics affecting survival in GBM using a large cancer registry database, the Surveillance Epidemiology End Results (SEER) registry, and identify strategies to reduce risk and disparities for patients with GBM. METHODS Individual-level data were obtained from SEER 18 program (1997-2016) using SEER*Stat software. New variables on urban-rural area and treatment combination among surgery, radiotherapy, and chemotherapy were created to comprehensively identify determinants affecting survival in GBM. Univariate and multivariate survival analyses were performed to estimate median survival time using Kaplan-Meier methods and to evaluate the relative risks of potential determinants using Cox hazard methods. RESULTS (1) The important determinants include age, gender, race, rural-urban area, diagnostic confirmation, tumor size, resection type, metastases, laterality, treatment effects and combined effects. (2) In addition to the standard treatment on GBM, the socio-demographic and clinical factors like rural-urban area (access to hospital), diagnostic conformation, and report type were important to reduce the risk to GBM patients. (3) Coming to modern times, survival time and survival rate have improved, especially in terms of socio-economic factors of people living in metro areas and married people (HR = 0.897 to 0.813 for metro area and HR = 0.999 to 0.918 for married status). CONCLUSIONS Our findings of higher risk determinants in GBM might lead to better prognosis in GBM with socio-demographic and clinical factors affecting the survival in GBM. The future investigation including MGMT promoter methylation might be beneficial with better understanding of determinants affecting risk in GBM.
BIOM-30. ANALYSIS OF GLIOMA-RELATED GENES USING A BREAKTHROUGH AMPLIFICATION TECHNIQUE FOR CELL-FREE DNA IN CEREBROSPINAL FLUID
Authors: Jun-ichi Adachi, Kazuhiko Mishima, Ryo Nishikawa
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND In the pathological classification of brain tumors, newly revised in 2021, molecular genetic analysis of gliomas has become more important for diagnosis and understanding of the pathogenesis of the disease. Gliomas are prone to recurrence and malignant progression, and collecting tumor tissue during every genetic analysis is highly invasive. Therefore, techniques have been developed to analyze tumor-derived circulating cell-free DNA (ccfDNA) in the cerebrospinal fluid as a substitute for tissue collection. However, the amount of ccfDNA derived from the cerebrospinal fluid is extremely small and the number of cases for whom genetic analysis is possible is currently limited. In this study, we attempted to establish an efficient method for the integrated analysis of glioma-related genes by in vitro amplification of cerebrospinal fluid-derived ccfDNA from glioma patients and a highly sensitive assay. METHODS Tumor-derived ccfDNA was extracted and purified from 1 ml of cerebrospinal fluid obtained by lumbar puncture using the Maxwell RSC instrument in five glioma cases. Hot spots of mutations in IDH1 and H3F3A genes were analyzed by high resolution melting (HRM), TERT mutation by droplet digital PCR, MGMT promoter methylation by methylation-specific HRM, and chromosome 1p/19q loss by multiplex ligation-dependent probe amplification. For samples in which the amount of ccfDNA was too small to analyze, DNA was amplified approximately 500-fold by DNA polymerase using the GenomiPhi kit and analyzed by the same assay method. RESULTS AND CONCLUSIONS Although two of the five cases required amplification with the GenomiPhi kit, it was possible to analyze all cases for glioma-related genes as described above. Although the amount of ccfDNA obtained from low-grade gliomas and gliomas that are not in contact with the ventricles or subarachnoid space is small, this amplification method may increase the possibility of liquid biopsy using cerebrospinal fluid.
EPCO-45. EXTRACHROMOSOMAL DNA PROMOTES ONCOGENE AMPLIFICATION ACROSS MULTIPLE PEDIATRIC CANCER TYPES
Authors: Sunita Sridhar, Owen Chapman, Aditi Dutta, Shanqing Wang, Lukas Chavez
Journal: Neuro-Oncology (2022)

Abstract Extrachromosomal circular DNA (ecDNA) is an important driver of aggressive cancers. Its frequency and impact on pediatric cancers has yet to be fully described. To determine the ecDNA prevalence in various pediatric cancer types, we accessed whole genome sequencing (WGS) data in the Children’s Brain Tumor Network (CBTN) and St. Jude cancer cloud genomics platforms and utilized the bioinformatics tools Amplicon Architect (AA) and Amplicon Classifier (AC) to reconstruct ecDNA sequence structures. We then identified which genes were amplified on the ecDNA and how ecDNA correlated with survival, using Kaplan Meier curves. Different cancer types were noted to have varying prevalence of ecDNA with the highest detection in pediatric high-grade gliomas (30% of cases). In analyzing matched diagnostic/relapse and relapse/progression pairs, ecDNA was noted to evolve over time with progression of disease. Our preliminary results demonstrate that ecDNA is prevalent in pediatric cancer, can contain known and potential novel oncogenes and can be associated with poorer outcomes across many different pediatric cancer types.